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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Rhodospirillum centenum (strain ATCC 51521 / SW)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan.UniRule annotation

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.UniRule annotation

Pathwayi: L-lysine biosynthesis via DAP pathway

This protein is involved in step 1 of the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Diaminopimelate epimerase (dapF)
This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei13SubstrateUniRule annotation1
Binding sitei46SubstrateUniRule annotation1
Binding sitei66SubstrateUniRule annotation1
Active sitei75Proton donor/acceptorUniRule annotation1
Binding sitei156SubstrateUniRule annotation1
Sitei158Important for catalytic activityUniRule annotation1
Binding sitei189SubstrateUniRule annotation1
Sitei207Important for catalytic activityUniRule annotation1
Active sitei216Proton donor/acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimeraseUniRule annotation (EC:5.1.1.7UniRule annotation)
Short name:
DAP epimeraseUniRule annotation
Gene namesi
Name:dapFUniRule annotation
Ordered Locus Names:RC1_2197
OrganismiRhodospirillum centenum (strain ATCC 51521 / SW)
Taxonomic identifieri414684 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodospirillalesRhodospirillaceaeRhodospirillum
Proteomesi
  • UP000001591 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10001244291 – 291Diaminopimelate epimeraseAdd BLAST291

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi75 ↔ 216

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi414684.RC1_2197.

Structurei

3D structure databases

ProteinModelPortaliB6IP82.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni10 – 11Substrate bindingUniRule annotation2
Regioni75 – 77Substrate bindingUniRule annotation3
Regioni207 – 208Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiRFTKMQG.
OrthoDBiPOG091H01QC.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

B6IP82-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVRRFLKMHG LGNDFVVLDA RRDPLPLTTA AARAIADRHT GVGCDQIVLL
60 70 80 90 100
EPPRHPAADL FMRILNPDGS ESGACGNATR CVASLVADGS GRAEVTVETA
110 120 130 140 150
TGLLRCRLRA DGSVTVDMGP ARLDWTQIPL AAAHDTLRVP AGAGPLQDAC
160 170 180 190 200
CVGMGNPHAV FFVDDAEAVD LATLGPVLEH HSLFPQRCNI EVAQVLAPDH
210 220 230 240 250
IRMRVWERGA GITRACGSGS CATLVAAARR GLTGRAAWIE LDGGRLWIEW
260 270 280 290
HGDGHVLMTG PVATAFTGEL SETLLPGSLP SETPLPETVP A
Length:291
Mass (Da):30,704
Last modified:December 16, 2008 - v1
Checksum:i0B546D7062B5895C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000613 Genomic DNA. Translation: ACI99584.1.
RefSeqiWP_012567369.1. NC_011420.2.

Genome annotation databases

EnsemblBacteriaiACI99584; ACI99584; RC1_2197.
KEGGirce:RC1_2197.
PATRICi23319582. VBIRhoCen1465_2127.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000613 Genomic DNA. Translation: ACI99584.1.
RefSeqiWP_012567369.1. NC_011420.2.

3D structure databases

ProteinModelPortaliB6IP82.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi414684.RC1_2197.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACI99584; ACI99584; RC1_2197.
KEGGirce:RC1_2197.
PATRICi23319582. VBIRhoCen1465_2127.

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiRFTKMQG.
OrthoDBiPOG091H01QC.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDAPF_RHOCS
AccessioniPrimary (citable) accession number: B6IP82
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: December 16, 2008
Last modified: November 2, 2016
This is version 51 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.